In What Ways Can The Owl Format Be Preferrable To Tab-Delimited Files?

Question

[rolyata47]

I am reading up on Pathways Commons as well as their BioPax java tool. The first question that comes to mind when reading this is - why come up with a new data format (the OWL format), when tab-delimited files work fine?

It seems to me that the simplest way to exchange data is in a set of tab-delimited files from a reliable database, and an ER diagram that explains the relations between these files (soon to be tables). DBSNP did a good job with this, for instance, as they provide a vast set of tables that allow you, if you are interested, to create a partial local copy from a limited set.

So if we are to complicate the exchange of data with a new format, requiring a Java tool to extract data, what new advantages does it bring to justify the loss of straightforwardness?

And seeing how PathwayCommons provides both OWL files and tab-delimited files, what is the best way to create a local copy in a relational database? They advocate the OWL format in their README file, but it would seem a bit simpler to use the tab-delimited files.

Keep in mind I'm a programmer and not a biologist! Thanks for any feedback.

[Michael]

Did you read about the OWL format and the rationale behind it? http://www.w3.org/TR/2004/REC-owl-features-20040210/#s1.2 and http://www.w3.org/TR/owl2-overview/ OWL wasn't just something Pathway Commons came up with but it is a standard format for ontologies recommended by the w3c

[rolyata47]

Ah, I see, thanks.

[Egon Willighagen]

Did you try to recreate the OWL file from the TSV file and macthing ER diagram using a program you wrote. Did that work?

Answer 1

[Pierre Lindenbaum]

OWL is a language to describe the data. It is based on RDF but, as far as I know, nothing is said that RDF/OWL should/must be described using XML.

(example via wikipedia)

<rdf:RDF xmlns:rdf="&lt;a href=" http:="" www.w3.org="" 1999="" 02="" 22-rdf-syntax-ns#"="" rel="nofollow">http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:dc="http://purl.org/dc/elements/1.1/">
  <rdf:Description rdf:about="&lt;a href=" http:="" en.wikipedia.org="" wiki="" Tony_Benn"="" rel="nofollow">http://en.wikipedia.org/wiki/Tony_Benn">
    <dc:title>Tony Benn</dc:title>
    <dc:publisher>Wikipedia</dc:publisher>
  </rdf:Description>
</rdf:RDF>

is the very same as:

<http://en.wikipedia.org/wiki/Tony_Benn> <http://purl.org/dc/elements/1.1/title> "Tony Benn";
<http://en.wikipedia.org/wiki/Tony_Benn> <http://purl.org/dc/elements/1.1/publisher> "Wikipedia".

BUT using one of those format make it already available for any RDF-based tool (parser,reasoner, etc...)

Answer 2

[mikel.egana.aranguren]

OWL is not a data format. It is a Knowledge Representation language that can be used to build ontologies that represent a domain of knowledge with precise semantics and therefore in a computer friendly fashion, for automated reasoning, querying, consistency checking, etc. In this case, OWL is used to build a concrete ontology, namley BioPax, that unambigiosuly describes the meaning of Pathway data. Also, OWL is (Semantic) Web oriented: URIs, etc.